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ms-finder website  

MS-FINDER was launched as a universal program for compound ‘annotation’ that supports EI-MS (GC/MS) and MS/MS spectral mining.

First, MS-FINDER aims to provide solutions for

  • formula predictions
  • fragment annotations
  • structure elucidations by means of unknown spectra

In addition, the program can annotate your unknowns by the public spectral databases such as MassBank, LipidBlast, and GNPS.

Additional Information

This program is not usable in a shared Linux environment because it attempts to open reference data/configuration files in a read and write modes even though it only needs to read them. Until the program is fixed, if you need to use MsfinderConsoleApp you will have to download and unzip the distribution into your personal directory and run the program from there.


If you publish research that uses ms-finder you have to cite it as follows:

Hydrogen rearrangement rules: computational MS/MS fragmentation and structure elucidation using MS-FINDER software. Analytical Chemistry 88, 7946-7958, 2016.

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods, 15, 53-56, 2018.